Abstract

Background

Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was
used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant
Germplasm System in the USA. The collection includes inbred lines from breeding programs
all over the world.

Results

The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed
across the entire genome, with the ability to detect rare alleles at high confidence
levels. More than half of the SNPs in the collection are rare. Although most rare
alleles have been incorporated into public temperate breeding programs, only a modest
amount of the available diversity is present in the commercial germplasm. Analysis
of genetic distances shows population stratification, including a small number of
large clusters centered on key lines. Nevertheless, an average fixation index of 0.06
indicates moderate differentiation between the three major maize subpopulations. Linkage
disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent
on the particular group of germplasm and region of the genome. The utility of these
data for performing genome-wide association studies was tested with two simply inherited
traits and one complex trait. We identified trait associations at SNPs very close
to known candidate genes for kernel color, sweet corn, and flowering time; however,
results suggest that more SNPs are needed to better explore the genetic architecture
of complex traits.

Conclusions

The genotypic information described here allows this publicly available panel to be
exploited by researchers facing the challenges of sustainable agriculture through
better knowledge of the nature of genetic diversity.